Tag: kegg

KEGG ORTHOLOGY: K06625

Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing  09132 Signal transduction   04012 ErbB signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04630 JAK-STAT signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04066 HIF-1 signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04068 FoxO signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04151 PI3K-Akt signaling pathway    K06625  CDKN1A, P21,…

Continue Reading KEGG ORTHOLOGY: K06625

KEGG COMPOUND: C05924

KEGG COMPOUND: C05924     COMPOUND: C05924 Help Entry C05924                      Compound                                Name Molybdopterin;Pyranopterin;H2Dtpp-mP Formula C10H14N5O6PS2 Exact mass 395.0123 Mol weight 395.3518 Structure Mol fileKCF fileDB search Reaction Pathway Module M00880   Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor Enzyme Other DBs KCF data Show ATOM        24            1   S1a S    22.7500  -13.4003            2   S1a S    25.1308  -14.8087            3   C2y C    22.7383  -14.7666            4   C2y C    23.9353  -15.4866            5   C1y C    21.5555  -15.4809            6   C1y C    23.9236  -16.8776            7   C1y C    21.5496  -16.8718            8   N1x N    20.3269  -14.7608            9   C1b…

Continue Reading KEGG COMPOUND: C05924

MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

Continue Reading MND1 Expression as a Predictor of Breast Cancer Survival

Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

Continue Reading Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS  Article  PubMed  Google Scholar  El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS  Article …

Continue Reading Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population

This article was originally published here Genes (Basel). 2022 Mar 28;13(4):601. doi: 10.3390/genes13040601. ABSTRACT Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have…

Continue Reading Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population

KEGG COMPOUND: C05345

KEGG COMPOUND: C05345     COMPOUND: C05345 Help Entry C05345                      Compound                                Name beta-D-Fructose 6-phosphate;beta-D-Fructofuranose 6-phosphate Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map00010   Glycolysis / Gluconeogenesis map00051   Fructose and mannose metabolism map00520   Amino sugar and nucleotide sugar metabolism map00541   O-Antigen nucleotide sugar biosynthesis map00997  …

Continue Reading KEGG COMPOUND: C05345

Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

Background: Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circRNAs play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed…

Continue Reading Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

KEGG MODULE: M00567

    MODULE: M00567 Help Entry M00567            Pathway   Module                                  Name Methanogenesis, CO2 => methane Definition (K00200+K00201+K00202+K00203-K11261+(K00205,K11260,K00204)) K00672 K01499 (K00319,K13942) K00320 (K00577+K00578+K00579+K00580+K00581-K00582-K00583+K00584) (K00399+K00401+K00402) (K22480+K22481+K22482,K03388+K03389+K03390,K08264+K08265,K03388+K03389+K03390+K14127+(K14126+K14128,K22516+K00125)) Diagram Orthology   4Fe-4S ferredoxin formylmethanofuran–tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101] [RN:R03390] methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27] [RN:R03464] methylenetetrahydromethanopterin dehydrogenase [EC:1.5.99.9] [RN:R04456] 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] [RN:R04455] coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [EC:1.5.99.11] [RN:R04464] Ortholog tableTaxonomyModule table…

Continue Reading KEGG MODULE: M00567

N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

Continue Reading N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

A hypoxia-related signature in lung squamous cell carcinoma

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

Continue Reading A hypoxia-related signature in lung squamous cell carcinoma

Bioconductor – keggorthology

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see keggorthology. graph support for KO, KEGG Orthology Bioconductor version: 2.13 graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused…

Continue Reading Bioconductor – keggorthology

Bioconductor – neaGUI

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…

Continue Reading Bioconductor – neaGUI

Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

Continue Reading Bioinformatics analysis identifies widely expressed genes

A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens

Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS  Google Scholar  Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….

Continue Reading A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens

Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients

This article was originally published here Zhonghua Xin Xue Guan Bing Za Zhi. 2022 Mar 24;50(3):249-256. doi: 10.3760/cma.j.cn112148-20210106-00015. ABSTRACT Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF….

Continue Reading Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients

KEGG COMPOUND: C01380

Entry C01380                      Compound                                Name Ethylene glycol;1,2-Ethanediol;Ethane-1,2-diol Formula C2H6O2 Exact mass 62.0368 Mol weight 62.0678 Structure Mol fileKCF fileDB search Reaction Pathway map00625   Chloroalkane and chloroalkene degradation map00630   Glyoxylate and dicarboxylate metabolism map01120   Microbial metabolism in diverse environments Enzyme Other DBs KCF data Show ATOM        4            1   C1b C    28.1392  -16.3327            2   C1b C    29.5408  -16.3327            3   O1a O    27.4444  -17.5473            4   O1a O    30.2356  -17.5473BOND        3            1     1   2 1            2     1   3 1            3     2   4 1…

Continue Reading KEGG COMPOUND: C01380

Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

Continue Reading Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

KEGG REACTION: R01627

KEGG REACTION: R01627     REACTION: R01627 Help Entry R01627                      Reaction                                Name 3-dehydroshikimate hydro-lyase Definition 3-Dehydroshikimate <=> 3,4-Dihydroxybenzoate + H2O Equation Reaction class Enzyme Pathway rn01053   Biosynthesis of siderophore group nonribosomal peptides rn01110   Biosynthesis of secondary metabolites Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source…

Continue Reading KEGG REACTION: R01627

KEGG COMPOUND: C02538

KEGG COMPOUND: C02538     COMPOUND: C02538 Help Entry C02538                      Compound                                Name Formula C18H22O5S Exact mass 350.1188 Mol weight 350.4293 Structure Mol fileKCF fileDB search Reaction Pathway map00140   Steroid hormone biosynthesis Enzyme Brite Compounds with biological roles [BR:br08001] Hormones and transmitters  Steroid hormones   Estrogens    C02538  Estrone 3-sulfateLipids [BR:br08002] ST  Sterol lipids  ST02 Steroids   ST0201 C18 steroids (estrogens) and derivatives    C02538  Estrone 3-sulfate  ST05 Steroid…

Continue Reading KEGG COMPOUND: C02538

Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

Continue Reading Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

Continue Reading Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis

KEGG ORTHOLOGY: K13942

KEGG ORTHOLOGY: K13942     ORTHOLOGY: K13942 Help Entry K13942                      KO                                      Symbol hmd Name 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] Pathway map01120   Microbial metabolism in diverse environments Module M00567   Methanogenesis, CO2 => methane Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09102 Energy metabolism   00680 Methane metabolism    K13942  hmd; 5,10-methenyltetrahydromethanopterin hydrogenaseEnzymes [BR:ko01000] 1. Oxidoreductases  1.12  Acting on hydrogen as donor   1.12.98  With other, known, physiological acceptors    1.12.98.2  5,10-methenyltetrahydromethanopterin…

Continue Reading KEGG ORTHOLOGY: K13942

Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

Continue Reading Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

Continue Reading Identification of Hub Genes Associated with COPD Through Integrated Bi

KEGG COMPOUND: C01113

KEGG COMPOUND: C01113     COMPOUND: C01113 Help Entry C01113                      Compound                                Name D-Galactose 6-phosphate;6-Phospho-D-galactose Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map02060   Phosphotransferase system (PTS) Enzyme Other DBs KCF data Show ATOM        16            1   P1b P    25.9015  -16.0011            2   O2b O    27.3009  -16.0070            3   O1c O    25.8898  -17.4005            4   O1c O    24.5021  -16.0011            5   O1c O    25.8898  -14.6076            6   C1b C    28.3679  -15.0973            7   C1y C    29.5748  -15.8029            8   C1y C    29.5748  -17.2021            9   O2x O    30.7818  -15.0973            10  C1y C    30.7818  -17.9018            11  O1a O    28.3679  -17.9018            12  C1y C    32.0005  -15.8029            13  C1y…

Continue Reading KEGG COMPOUND: C01113

KEGG COMPOUND: C00469

KEGG COMPOUND: C00469     COMPOUND: C00469 Help Entry C00469                      Compound                                Name Ethanol;Ethyl alcohol;Methylcarbinol Formula C2H6O Exact mass 46.0419 Mol weight 46.0684 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00010   Glycolysis / Gluconeogenesis map01110   Biosynthesis of secondary metabolites map01120   Microbial metabolism in diverse environments map04750   Inflammatory mediator regulation of TRP channels…

Continue Reading KEGG COMPOUND: C00469

KEGG T01001: 5105

Entry 5106              CDS       T01001                                  Symbol PCK2, PEPCK, PEPCK-M, PEPCK2 Name (RefSeq) phosphoenolpyruvate carboxykinase 2, mitochondrial   KO K01596   phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32] Organism hsa  Homo sapiens (human) Pathway hsa00010   Glycolysis / Gluconeogenesis hsa00020   Citrate cycle (TCA cycle) hsa00620   Pyruvate metabolism hsa01100   Metabolic pathways hsa03320   PPAR signaling pathway hsa04068   FoxO signaling pathway hsa04151   PI3K-Akt signaling…

Continue Reading KEGG T01001: 5105

KEGG COMPOUND: C00565

Entry C00565                      Compound                                Name Trimethylamine;(CH3)3N;N,N-Dimethylmethanamine Formula C3H9N Exact mass 59.0735 Mol weight 59.1103 Structure Mol fileKCF fileDB search Reaction Pathway map01120   Microbial metabolism in diverse environments Module M00563   Methanogenesis, methylamine/dimethylamine/trimethylamine => methane Enzyme Other DBs KCF data Show ATOM        4            1   N1c N    22.1200  -15.8200            2   C1a C    23.3299  -15.1185            3   C1a C    20.9101  -15.1185            4   C1a C    22.1200  -17.2929BOND        3            1     1   2 1            2     1   3 1            3     1   4 1 Read more here: Source link

Continue Reading KEGG COMPOUND: C00565

Workflow Platforms for Systems Genetics

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

Continue Reading Workflow Platforms for Systems Genetics

KEGG ENZYME: 2.7.2.1

Entry EC 2.7.2.1                  Enzyme                                  Name acetate kinase;acetokinase;AckA;AK;acetic kinase;acetate kinase (phosphorylating) Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with a carboxy group as acceptorBRITE hierarchy Sysname ATP:acetate phosphotransferase Reaction(IUBMB) ATP + acetate = ADP + acetyl phosphate [RN:R00315] Reaction(KEGG) Substrate Product Comment Requires Mg2+ for activity. While purified enzyme from Escherichia coli is specific for acetate…

Continue Reading KEGG ENZYME: 2.7.2.1

KEGG COMPOUND: C00247

KEGG COMPOUND: C00247     COMPOUND: C00247 Help Entry C00247                      Compound                                Name L-Sorbose;L-xylo-Hexulose Formula C6H12O6 Exact mass 180.0634 Mol weight 180.1559 Structure Mol fileKCF fileDB search Comment Reaction Pathway map00051   Fructose and mannose metabolism Enzyme Brite Compounds with biological roles [BR:br08001] Carbohydrates  Monosaccharides   Ketoses    C00247  L-Sorbose BRITE hierarchy Other DBs KCF data Show ATOM        12            1   C1z C    26.2968  -14.4371            2   C1y C    26.2968  -15.8376            3   O2x O    25.0888  -13.7368            4   C1b…

Continue Reading KEGG COMPOUND: C00247

Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

Continue Reading Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

This article was originally published here Hematology. 2022 Dec;27(1):280-292. doi: 10.1080/16078454.2022.2040123. ABSTRACT PURPOSE: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease…

Continue Reading Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

Continue Reading Validation of hub genes in acute pancreatitis

KEGG COMPOUND: C21620

KEGG COMPOUND: C21620     COMPOUND: C21620 Help Entry C21620                      Compound                                Name S-[(E)-N-Hydroxy(indol-3-yl)acetimidoyl]-L-glutathione Formula C20H25N5O7S Exact mass 479.1475 Mol weight 479.5068 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM        33            1   C8y C    17.0403  -15.7134            2   C8y C    18.3672  -15.9928            3   C8y C    16.3420  -16.9006            4   C8x C    16.3420  -14.4564            5   C8x C    18.4371  -17.3895            6   N4x N    17.1800  -17.9482            7   C8x C    14.8754  -16.9006            8   C8x C    14.9452  -14.4564            9   C8x C    14.1770  -15.7134            10  O1b O    19.6829  -18.0281            11  N2b N    20.8589  -17.2684            12  C2c C    20.7891  -15.8717            13  C1b C    19.5432  -15.2331            14  C1b C    23.2109  -15.7506            15  S2a S    21.9650  -15.1120            16  C1c C    24.3869  -14.9909            17  N1b N    24.3170  -13.5927            18  C5a C    25.6328  -15.6295            19  O5a…

Continue Reading KEGG COMPOUND: C21620

Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

Continue Reading Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

Continue Reading Fatty infiltration after rotator cuff tear

KEGG T03334: R50912_07385

Entry R50912_23945      CDS       T03334                                  Name (GenBank) alpha-galactosidase   KO K07407   alpha-galactosidase [EC:3.2.1.22] Organism paeq  Paenibacillus sp. FSL R5-0912 Pathway paeq00052   Galactose metabolism paeq00561   Glycerolipid metabolism paeq00600   Sphingolipid metabolism paeq01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:paeq00001] 09100 Metabolism  09101 Carbohydrate metabolism   00052 Galactose metabolism    R50912_23945  09103 Lipid metabolism   00561 Glycerolipid metabolism    R50912_23945   00600 Sphingolipid metabolism    R50912_23945Enzymes [BR:paeq01000] 3. Hydrolases  3.2  Glycosylases   3.2.1  Glycosidases, i.e. enzymes that hydrolyse O-…

Continue Reading KEGG T03334: R50912_07385

KEGG ENZYME: 2.4.1.81

Entry EC 2.4.1.81                 Enzyme                                  Name flavone 7-O-beta-glucosyltransferase;UDP-glucose-apigenin beta-glucosyltransferase;UDP-glucose-luteolin beta-D-glucosyltransferase;uridine diphosphoglucose-luteolin glucosyltransferase;uridine diphosphoglucose-apigenin 7-O-glucosyltransferase;UDP-glucosyltransferase (ambiguous) Class Transferases;Glycosyltransferases;HexosyltransferasesBRITE hierarchy Sysname UDP-glucose:5,7,3′,4′-tetrahydroxyflavone 7-O-beta-D-glucosyltransferase Reaction(IUBMB) UDP-glucose + 5,7,3′,4′-tetrahydroxyflavone = UDP + 7-O-beta-D-glucosyl-5,7,3′,4′-tetrahydroxyflavone [RN:R03588] Reaction(KEGG) Substrate UDP-glucose [CPD:C00029]; 5,7,3′,4′-tetrahydroxyflavone [CPD:C01514] Product UDP [CPD:C00015]; 7-O-beta-D-glucosyl-5,7,3′,4′-tetrahydroxyflavone [CPD:C03951] Comment A number of flavones, flavanones and flavonols can function as acceptors….

Continue Reading KEGG ENZYME: 2.4.1.81

KEGG REACTION: R02703

KEGG REACTION: R02703     REACTION: R02703 Help Entry R02703                      Reaction                                Name D-Mannitol-1-phosphate:NAD+ 5-oxidoreductase Definition D-Mannitol 1-phosphate + NAD+ <=> beta-D-Fructose 6-phosphate + NADH + H+ Equation Reaction class Enzyme Pathway rn00051   Fructose and mannose metabolism Orthology LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link

Continue Reading KEGG REACTION: R02703

KEGG ENZYME: 2.2.1.4

KEGG ENZYME: 2.2.1.4     ENZYME: 2.2.1.4 Help Entry EC 2.2.1.4                  Enzyme                                  Name acetoin—ribose-5-phosphate transaldolase;1-deoxy-D-altro-heptulose-7-phosphate synthetase;1-deoxy-D-altro-heptulose-7-phosphate synthase;3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase [wrong substrate name] Class Transferases;Transferring aldehyde or ketonic groups;Transketolases and transaldolasesBRITE hierarchy Sysname 3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase Reaction(IUBMB) 3-hydroxybutan-2-one + D-ribose 5-phosphate = acetaldehyde + 1-deoxy-D-altro-heptulose 7-phosphate [RN:R02345] Reaction(KEGG) Substrate 3-hydroxybutan-2-one [CPD:C00466]; D-ribose 5-phosphate [CPD:C00117] Product acetaldehyde…

Continue Reading KEGG ENZYME: 2.2.1.4

KEGG REACTION: R03385

KEGG REACTION: R03385     REACTION: R03385 Help Entry R03385                      Reaction                                Name 3-hydroxy-2-methylpyridine-5-carboxylate,NADH:oxygen oxidoreductase (ring-opening) Definition 3-Hydroxy-2-methylpyridine-5-carboxylate + Oxygen + NADH + H+ <=> 2-(Acetamidomethylene)succinate + NAD+ Equation Comment Reaction class Enzyme Pathway rn01120   Microbial metabolism in diverse environments Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more…

Continue Reading KEGG REACTION: R03385

KEGG COMPOUND: C06070

KEGG COMPOUND: C06070     COMPOUND: C06070 Help Entry C06070                      Compound                                Name Iridotrial;(1S,2R,3S)-2-Formyl-alpha-(hydroxymethylene)-3-methylcyclopentaneacetaldehyde Formula C10H14O3 Exact mass 182.0943 Mol weight 182.2164 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Enzyme Brite Lipids [BR:br08002] PR  Prenol lipids  PR01 Isoprenoids   PR0102 C10 isoprenoids (monoterpenes)    PR010207 Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids     C06070  IridotrialPhytochemical compounds [BR:br08003] Terpenoids  Monoterpenoids (C10)   Iridoids    C06070  Iridotrial BRITE hierarchy…

Continue Reading KEGG COMPOUND: C06070

Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that play important roles in human diseases. However, the regulation of circRNAs in glucocorticoid-induced osteoporosis (GIOP) has not been reported. In this study, we performed high-throughput sequencing to identify altered circRNAs in the vertebrae from GIOP patients. A total of…

Continue Reading Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism

Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

Continue Reading Identification of a four-gene signature & PTC.

How to do functional analysis on differentially expressed gene list from RNA-seq data?

How to do functional analysis on differentially expressed gene list from RNA-seq data? 0 @06f08eeb Last seen 1 day ago Canada Hi all, I am a complete beginner in terms of bioinformatics analysis and I am hoping to complete some functional analysis on some differentially expressed gene lists of some…

Continue Reading How to do functional analysis on differentially expressed gene list from RNA-seq data?

KEGG REACTION: R00481

KEGG REACTION: R00481     REACTION: R00481 Help Entry R00481                      Reaction                                Name L-aspartate:oxygen oxidoreductase Definition L-Aspartate + Oxygen <=> Iminoaspartate + Hydrogen peroxide Equation Comment Reaction class Enzyme Pathway rn00760   Nicotinate and nicotinamide metabolism rn01240   Biosynthesis of cofactors Module M00115   NAD biosynthesis, aspartate => quinolinate => NAD Orthology Other DBs LinkDB All…

Continue Reading KEGG REACTION: R00481

Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

Continue Reading Novel diagnostic biomarkers for keloid based on GEO database

KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

Continue Reading KEGG T00007: b1542

KEGG REACTION: R00226

Entry R00226                      Reaction                                Name pyruvate:pyruvate acetaldehydetransferase (decarboxylating);(S)-2-acetolactate pyruvate-lyase (carboxylating) Definition (S)-2-Acetolactate + CO2 <=> 2 Pyruvate Equation Comment Reaction class Enzyme Pathway rn00290   Valine, leucine and isoleucine biosynthesis rn00660   C5-Branched dibasic acid metabolism rn00770   Pantothenate and CoA biosynthesis rn01110   Biosynthesis of secondary metabolites rn01210   2-Oxocarboxylic acid metabolism rn01230   Biosynthesis of amino…

Continue Reading KEGG REACTION: R00226

Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS  Article  PubMed  Google Scholar  Altamirano C, Illanes A, Casablancas A, Gámez X,…

Continue Reading Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

KEGG ENZYME: 3.1.3.96

Entry EC 3.1.3.96                 Enzyme                                  Name pseudouridine 5′-phosphatase;pseudouridine 5′-monophosphatase;5′-PsiMPase;HDHD1 Class Hydrolases;Acting on ester bonds;Phosphoric-monoester hydrolasesBRITE hierarchy Sysname pseudouridine 5′-phosphohydrolase Reaction(IUBMB) pseudouridine 5′-phosphate + H2O = pseudouridine + phosphate [RN:R11180] Reaction(KEGG) R11180 Reaction Substrate pseudouridine 5′-phosphate [CPD:C01168]; H2O [CPD:C00001] Product pseudouridine [CPD:C02067]; phosphate [CPD:C00009] Comment Requires Mg2+ for activity. History EC 3.1.3.96 created 2014…

Continue Reading KEGG ENZYME: 3.1.3.96

KEGG REACTION: R03197

    REACTION: R03197 Help Entry R03197                      Reaction                                Name Uroporphyrinogen-III carboxy-lyase Definition Uroporphyrinogen III <=> Coproporphyrinogen III + 4 CO2 Equation Reaction class Enzyme Pathway rn01110   Biosynthesis of secondary metabolites rn01240   Biosynthesis of cofactors Module M00121   Heme biosynthesis, plants and bacteria, glutamate => heme M00868   Heme biosynthesis, animals and fungi, glycine =>…

Continue Reading KEGG REACTION: R03197

KEGG PATHWAY: map00051

Entry map00051                    Pathway                                 Name Fructose and mannose metabolism Class Metabolism; Carbohydrate metabolismBRITE hierarchy Pathway map map00051   Fructose and mannose metabolism Ortholog table Module M00114   Ascorbate biosynthesis, plants, fructose-6P => ascorbate [PATH:map00051] Other DBs Relatedpathway map00010   Glycolysis / Gluconeogenesis map00053   Ascorbate and aldarate metabolism map00520   Amino sugar and nucleotide sugar metabolism KO pathway Read…

Continue Reading KEGG PATHWAY: map00051

KEGG ENZYME: 6.5.1.9

Entry EC 6.5.1.9                  Enzyme                                  Name cyclic 2,3-diphosphoglycerate synthase;cpgS (gene name) Class Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)BRITE hierarchy Sysname (2R)-2,3-bisphosphoglycerate ligase (cyclizing) Reaction(IUBMB) ATP + 2,3-diphospho-D-glycerate = ADP + phosphate + cyclic 2,3-bisphosphoglycerate [RN:R03298] Reaction(KEGG) Substrate Product Comment The enzyme is present in a number of…

Continue Reading KEGG ENZYME: 6.5.1.9

Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

Continue Reading Immune-related Prognostic Genes of ccRCC

KEGG REACTION: R00750

Entry R00750                      Reaction                                Name 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming) Definition Acetaldehyde + Pyruvate <=> 4-Hydroxy-2-oxopentanoate Equation Reaction class Enzyme Pathway rn00360   Phenylalanine metabolism rn01120   Microbial metabolism in diverse environments rn01220   Degradation of aromatic compounds Module M00545   Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA M00569   Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA Orthology Other…

Continue Reading KEGG REACTION: R00750

Identification of differentially expressed genes in AF

Defeng Pan,1,&ast; Yufei Zhou,2,&ast; Shengjue Xiao,1,&ast; Yue Hu,3,&ast; Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

Continue Reading Identification of differentially expressed genes in AF

Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

Continue Reading Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

KEGG ORTHOLOGY: K11868

KEGG ORTHOLOGY: K11868     ORTHOLOGY: K11868 Help Entry K11868                      KO                                      Symbol CYP71A13 Name indoleacetaldoxime dehydratase [EC:4.8.1.3] Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09105 Amino acid metabolism   00380 Tryptophan metabolism    K11868  CYP71A13; indoleacetaldoxime dehydratase 09180 Brite Hierarchies  09181 Protein families: metabolism   00199 Cytochrome P450    K11868  CYP71A13; indoleacetaldoxime dehydrataseEnzymes [BR:ko01000] 4. Lyases  4.8  Nitrogen-oxygen lyases   4.8.1  Hydro-lyases    4.8.1.3  indoleacetaldoxime dehydratase     K11868  CYP71A13; indoleacetaldoxime dehydrataseCytochrome P450 [BR:ko00199] Cytochrome P450, plant type  CYP71 family   K11868  CYP71A13;…

Continue Reading KEGG ORTHOLOGY: K11868

biopython – Github Help

1 1 0 biopython,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

Continue Reading biopython – Github Help

KEGG ENZYME: 2.2.1.10

Entry EC 2.2.1.10                 Enzyme                                  Name 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase;ADH synthase;ADHS;MJ0400 (gene name) Class Transferases;Transferring aldehyde or ketonic groups;Transketolases and transaldolasesBRITE hierarchy Sysname L-aspartate 4-semialdehyde:1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate methylglyoxaltransferase Reaction(IUBMB) L-aspartate 4-semialdehyde + 1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate = 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate + 2,3-dioxopropyl phosphate [RN:R08568] Reaction(KEGG) Substrate L-aspartate 4-semialdehyde [CPD:C00441]; 1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate [CPD:C16848] Product 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate; 2,3-dioxopropyl phosphate [CPD:C16849] Comment The enzyme…

Continue Reading KEGG ENZYME: 2.2.1.10

KEGG T01005: 453503

Entry 453503            CDS       T01005                                  Symbol SNX1 Name (RefSeq) sorting nexin-1 isoform X3   KO K17917   sorting nexin-1/2 Organism ptr  Pan troglodytes (chimpanzee) Pathway ptr04144   Endocytosis Brite KEGG Orthology (KO) [BR:ptr00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    453503 (SNX1) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:ptr04131]    453503 (SNX1)  09183 Protein families: signaling and cellular processes   04990…

Continue Reading KEGG T01005: 453503

kegg – Github Help

1 1 0 kegg,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

Continue Reading kegg – Github Help

Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

Continue Reading Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome

Significance Cu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme, and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress; metabolic defects; and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2•−) in a manner that…

Continue Reading Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome

KEGG COMPOUND: C09877

KEGG COMPOUND: C09877     COMPOUND: C09877 Help エントリ   C09877                      Compound                                名称     (+)-β-フェランドレン;(+)-beta-Phellandrene 組成式    C10H16 質量     136.1252 分子量    136.234 構造式    Mol fileKCF fileDB search 階層分類   Lipids [BR:br08002] PR  Prenol lipids  PR01 Isoprenoids   PR0102 C10 isoprenoids (monoterpenes)    PR010209 Menthane monoterpenoids     C09877  (+)-beta-PhellandrenePhytochemical compounds [BR:br08003] Terpenoids  Monoterpenoids (C10)   Cyclic monoterpenes    C09877  (+)-beta-Phellandrene BRITE hierarchy リンク    LinkDB     All DBs » English version DBGET integrated database retrieval system…

Continue Reading KEGG COMPOUND: C09877

KEGG ENZYME: 1.14.14.86

Entry EC 1.14.14.86               Enzyme                                  Name ent-kaurene monooxygenase;ent-kaurene oxidase (misleading) Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donorBRITE hierarchy Sysname ent-kaur-16-ene,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (hydroxylating) Reaction(IUBMB) ent-kaur-16-ene + 3 [reduced NADPH—hemoprotein…

Continue Reading KEGG ENZYME: 1.14.14.86

KEGG REACTION: R01800

Entry R01800                      Reaction                                Name CDP-diacylglycerol:L-serine 3-phosphatidyltransferase Definition CDP-diacylglycerol + L-Serine <=> CMP + Phosphatidylserine Equation Reaction class Enzyme Pathway rn00260   Glycine, serine and threonine metabolism rn00564   Glycerophospholipid metabolism rn01110   Biosynthesis of secondary metabolites Module M00093   Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE Orthology K00998   CDP-diacylglycerol—serine O-phosphatidyltransferase [EC:2.7.8.8] K17103   CDP-diacylglycerol—serine O-phosphatidyltransferase…

Continue Reading KEGG REACTION: R01800

KEGG ORTHOLOGY: K02207

Brite KEGG Orthology (KO) [BR:ko00001] 09120 Genetic Information Processing  09123 Folding, sorting and degradation   04120 Ubiquitin mediated proteolysis    K02207  UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 R 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04121 Ubiquitin system    K02207  UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 REnzymes [BR:ko01000] 2. Transferases  2.3  Acyltransferases   2.3.2  Aminoacyltransferases    2.3.2.23  E2 ubiquitin-conjugating enzyme     K02207  UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 RUbiquitin system [BR:ko04121] Ubiquitin-conjugating enzymes (E2)  Ubiquitin-conjugating…

Continue Reading KEGG ORTHOLOGY: K02207

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

Continue Reading Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…

Continue Reading Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

Continue Reading GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

KEGG ENZYME: 6.3.1.17

KEGG ENZYME: 6.3.1.17     ENZYME: 6.3.1.17 Help Entry EC 6.3.1.17                 Enzyme                                  Name beta-citrylglutamate synthase;NAAG synthetase I;NAAGS-I;RIMKLB (gene name) (ambiguous) Class Ligases;Forming carbon-nitrogen bonds;Acid-D-ammonia (or amine) ligases (amide synthases)BRITE hierarchy Sysname citrate:L-glutamate ligase (ADP-forming) Reaction(IUBMB) ATP + citrate + L-glutamate = ADP + phosphate + beta-citryl-L-glutamate [RN:R10677] Reaction(KEGG) Substrate Product Comment The enzyme,…

Continue Reading KEGG ENZYME: 6.3.1.17

Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

Continue Reading Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

KEGG COMPOUND: C20284

KEGG COMPOUND: C20284     COMPOUND: C20284 Help Entry C20284                      Compound                                Name Benzenediazonium;Benzenediazonium ion Formula C6H5N2 Exact mass 105.0453 Mol weight 105.1173 Structure Mol fileKCF fileDB search Pathway map05204   Chemical carcinogenesis – DNA adducts Other DBs LinkDB All DBs KCF data Show ATOM        8            1   C8y C    18.6066  -15.8364            2   C8x C    17.4048  -16.5269            3   C8x C    19.8279  -16.5269            4   N3a N    18.6003  -14.4425 #+            5   C8x C    17.4048  -17.9334            6   C8x C    19.8279  -17.9334            7   N3a N    20.3623  -13.3957            8   C8x C    18.6066  -18.6494BOND        8            1     1   2…

Continue Reading KEGG COMPOUND: C20284

Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

Continue Reading Adrenal aldosterone-producing adenoma | IJGM

Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

Continue Reading Establishment of sunitinib-resistant CDX model of ccRCC

KEGG REACTION: R01918

KEGG REACTION: R01918     REACTION: R01918 Help Entry R01918                      Reaction                                Name gamma-L-glutamyl-L-cysteinyl-glycine:spermidine amidase Definition Glutathionylspermidine + H2O <=> Glutathione + Spermidine Equation Reaction class Enzyme Pathway Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link

Continue Reading KEGG REACTION: R01918

KEGG COMPOUND: C20288

KEGG COMPOUND: C20288     COMPOUND: C20288 Help Entry C20288                      Compound                                Name Formula C13H12N4O4S Exact mass 320.0579 Mol weight 320.3238 Structure Mol fileKCF fileDB search Pathway map05204   Chemical carcinogenesis – DNA adducts Other DBs LinkDB All DBs KCF data Show ATOM        22            1   C8y C    17.1244  -16.4935            2   C8x C    17.1244  -17.8970            3   N5x N    18.3400  -18.5988            4   C8y C    19.5556  -17.8970            5   C8y C    19.5556  -16.4935            6   C8x C    18.3400  -15.7917            7   N5x N    20.8905  -18.3308            8   C8y C    21.7155  -17.1953            9   N4y N    20.8905  -16.0597            10  C8y C    15.9089  -15.7917            11  C8x C    15.9089  -14.3883            12  C8x…

Continue Reading KEGG COMPOUND: C20288

KEGG COMPOUND: C21642

KEGG COMPOUND: C21642     COMPOUND: C21642 Help Entry C21642                      Compound                                Name 4-Hydroxynonenal;4-Hydroxy-2-nonenal;4-HNE Formula C9H16O2 Exact mass 156.115 Mol weight 156.2221 Structure Mol fileKCF fileDB search Pathway Other DBs LinkDB All DBs KCF data Show ATOM        11            1   C1a C    13.1567  -15.1124            2   C1b C    14.3460  -15.8120            3   C1b C    15.6053  -15.1124            4   C1b C    16.7947  -15.8120            5   C1b C    17.9840  -15.1124            6   C1c C    19.2433  -15.8120            7   C2b C    20.4326  -15.1124            8   C2b C    21.6219  -15.8120            9   C4a C    22.8812  -15.1124            10  O4a O    24.0706  -15.8120            11  O1a O    19.2433  -17.2112BOND        10            1     1   2 1            2     2   3 1            3     3   4 1            4     4   5 1            5     5   6 1            6     6   7…

Continue Reading KEGG COMPOUND: C21642

Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

Continue Reading Prognosis Biomarkers via WGCNA in HCC

KEGG PATHWAY: Diterpenoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq)

Complete onlyIncluding 1 block missingIncluding any incomplete Pathway modules Biosynthesis of terpenoids and polyketides Plant terpenoid biosynthesis M00927 Gibberellin A12 biosynthesis M00928 Gibberellin A4/A1 biosynthesis M00929 Gibberellin A1 biosynthesis Read more here: Source link

Continue Reading KEGG PATHWAY: Diterpenoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq)

KEGG PATHWAY: Benzoxazinoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq)

KEGG PATHWAY: Benzoxazinoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq) [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] Benzoxazinoids (hydroxamic acids) are plant secondary metabolites that serve as important factors for host resistance against microbial pathogens and insects and for…

Continue Reading KEGG PATHWAY: Benzoxazinoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq)

KEGG ENZYME: 2.3.1.68

Entry EC 2.3.1.68                 Enzyme                                  Name glutamine N-acyltransferase Class Transferases;Acyltransferases;Transferring groups other than aminoacyl groupsBRITE hierarchy Sysname acyl-CoA:L-glutamine N-acyltransferase Reaction(IUBMB) acyl-CoA + L-glutamine = CoA + N-acyl-L-glutamine [RN:R00577] Reaction(KEGG) R00577 Reaction Substrate acyl-CoA [CPD:C00040]; L-glutamine [CPD:C00064] Product CoA [CPD:C00010]; N-acyl-L-glutamine [CPD:C02716] Comment Phenylacetyl-CoA and (indol-3-yl)acetyl-CoA, but not benzoyl-CoA, can act as acyl donors….

Continue Reading KEGG ENZYME: 2.3.1.68

KEGG ENZYME: 4.1.1.65

Entry EC 4.1.1.65                 Enzyme                                  Name phosphatidylserine decarboxylase;PS decarboxylase;phosphatidyl-L-serine carboxy-lyase Class Lyases;Carbon-carbon lyases;Carboxy-lyasesBRITE hierarchy Sysname phosphatidyl-L-serine carboxy-lyase (phosphatidylethanolamine-forming) Reaction(IUBMB) phosphatidyl-L-serine = phosphatidylethanolamine + CO2 [RN:R02055] Reaction(KEGG) Substrate phosphatidyl-L-serine [CPD:C02737] Product Comment A pyridoxal-phosphate protein. In Escherichia coli, the prosthetic group is a pyruvoyl group. History EC 4.1.1.65 created 1976 Pathway ec00564   Glycerophospholipid metabolism…

Continue Reading KEGG ENZYME: 4.1.1.65

Get data from KEGG Brite

Get data from KEGG Brite 0 Hi, I would like to retrieve all the interactions between ligands and target proteins from the KEGG BRITE database. Ideally, each entry will contain a protein name, a list of interacting ligands, its FASTA sequence and an sdf or mol2 coordinates of the ligand,…

Continue Reading Get data from KEGG Brite

KEGG PATHWAY: Fluorobenzoate degradation – Escherichia coli K-12 MG1655

[ Pathway menu | Pathway entry | Download KGML | Image (png) file | Help ] Option Scale: 100% Search ID search Color Read more here: Source link

Continue Reading KEGG PATHWAY: Fluorobenzoate degradation – Escherichia coli K-12 MG1655

Metabolite label to KEGG Id

Metabolite label to KEGG Id 0 Hi! I have a list of metabolite labels with associated values (metabolite A has been found in sample 1), as follows: metabolite_label value Total_C 4.605948787 non_HDL_C 3.598204496 Remnant_C 1.571938945 VLDL_C 0.808513241 Clinical_LDL_C 2.868314163 I want to use the Omu R package to do some…

Continue Reading Metabolite label to KEGG Id

KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655

KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655 [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA…

Continue Reading KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655

KEGG PATHWAY: Riboflavin metabolism – Oryza sativa japonica (Japanese rice) (RefSeq)

Complete onlyIncluding 1 block missingIncluding any incomplete Pathway modules Metabolism of cofactors and vitamins Cofactor and vitamin metabolism M00125 Riboflavin biosynthesis, plants and bacteria M00911 Riboflavin biosynthesis, fungi Read more here: Source link

Continue Reading KEGG PATHWAY: Riboflavin metabolism – Oryza sativa japonica (Japanese rice) (RefSeq)

Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

Continue Reading Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

Continue Reading Identification of lipid metabolism-associated gene signature

KEGG PATHWAY: Other glycan degradation

[ Pathway menu | Pathway entry | Download KGML | Image (png) file | Help ] Option Scale: 100% Search ID search Color Read more here: Source link

Continue Reading KEGG PATHWAY: Other glycan degradation

KEGG COMPOUND: C00766

KEGG COMPOUND: C00766     COMPOUND: C00766 Help Entry C00766                      Compound                                Name Flavanone;2,3-Dihydroflavone Formula C15H12O2 Exact mass 224.0837 Mol weight 224.2546 Structure Mol fileKCF fileDB search Comment Generic compound in reaction hierarchy Reaction Pathway map01060   Biosynthesis of plant secondary metabolites Enzyme Other DBs KCF data Show ATOM        17            1   C8x C     7.7700  -25.2700            2   C8x C     7.7700  -26.6700            3   C8x C     8.9824  -27.3700            4   C8y C    10.1949  -26.6700            5   C8y C    10.1949  -25.2700            6   C8x…

Continue Reading KEGG COMPOUND: C00766

Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

Continue Reading Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

KEGG PATHWAY: beta-Lactam resistance – Escherichia coli K-12 MG1655

KEGG PATHWAY: beta-Lactam resistance – Escherichia coli K-12 MG1655 [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] The beta-lactam antibiotics are the most widely used group of antibiotics, which exert their effect by interfering with the structural crosslinking of peptidoglycans in…

Continue Reading KEGG PATHWAY: beta-Lactam resistance – Escherichia coli K-12 MG1655

Index of /~psgendb/doc/local/zhangju/eclipse_project/Pl_MGCB2/Module_Dir

Name Last modified Size Description Parent Directory   –   Cazy_gbk_protein.pl 2015-11-09 14:56 2.5K   DataRetrieving.pl 2015-11-09 14:56 6.7K   GOshell.pl 2015-11-09 14:56 24K   ParseGffFile.pl 2015-11-09 14:56 17K   ParseKEGG.pl 2015-11-09 14:56 17K   Parse_Fasta.pl 2015-11-09 14:56 34K   Parse_Fastq.pl 2015-11-09 14:56 1.2K   Parse_Genbank.pl 2015-11-09 14:56 86K  …

Continue Reading Index of /~psgendb/doc/local/zhangju/eclipse_project/Pl_MGCB2/Module_Dir

KEGG COMPOUND: C21825

KEGG COMPOUND: C21825     COMPOUND: C21825 Help Entry C21825                      Compound                                Name 9beta-Pimara-7,15-diene-3beta-ol Formula C20H32O Exact mass 288.2453 Mol weight 288.4675 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Enzyme LinkDB All DBs KCF data Show ATOM        21            1   C1x C    14.9922  -16.1836            2   C1y C    14.9922  -17.5848            3   C1z C    16.1832  -18.2854            4   C1y C    17.4442  -17.5848            5   C1z C    17.4442  -16.1836            6   C1x C    16.1832  -15.4830            7   C1x C    18.6352  -18.2854            8   C2x C    19.8262  -17.5848            9   C2y C    19.8262  -16.1836            10  C1y C    18.6352  -15.4830            11  C1x C    21.0873  -15.4830            12  C1z…

Continue Reading KEGG COMPOUND: C21825